Remarkable Bacterial Diversity in the Tidal Flat Sediment as Revealed by 16S rDNA Analysis
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Chun, Jong-Sik
(School of Biological Sciences, Seoul National University)
Kim, Bong-Soo (School of Biological Sciences, Seoul National University) Oh, Huyn-Myung (School of Biological Sciences, Seoul National University) Kang, Ho-Jeong (Department of Environmental Science and Engineering, School of Engineering, Ewha Womans University) Park, Seok-Soon (Department of Environmental Science and Engineering, School of Engineering, Ewha Womans University) |
1 | Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143- 169 |
2 | Chun, J., A. Huq, and R. R. Colwell. 1999. Analysis of 16S- 23S rRNA intergenic spacer regions of Vibrio cholerae and Vibrio mimicus. Appl. Environ. Microbiol. 65: 2202-2208 |
3 | Cifuentes, A., J. Anton, S. Benlloch, A. Donnelly, R. A. Herbert, and F. Rodriguez-Valera. 2000. Prokaryotic diversity in Zostera noltii-colonized marine sediments. Appl. Environ. Microbiol. 66: 1715-1719 |
4 | Freitag, T. E. and J. I. Prosser. 2003. Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Appl. Environ. Microbiol. 69: 1359-1371 |
5 | Gray, J. P. and R. P. Herwig. 1996. Phylogenetic analysis of the bacterial communities in marine sediments. Appl. Environ. Microbiol. 62: 4049-4059 |
6 | Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366-376 |
7 | Hurst, C. J. 1997. Recovery of bacterial community DNA from soil, pp. 433-434. In Hurst, C. J., R. L. Crawford, G. R. Knudsen, M. J. McInerney and L. D. Stetzenbach (eds.), Manual of Environmental Microbiology, 2nd ed. ASM Press, Washington DC, U.S.A |
8 | Li, L., C. Kato, and K. Horikoshi. 1999. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar. Biotechnol. 1: 391-400 DOI |
9 | Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in atlantic and pacific bacterioplankton communities. Limnol. Oceanogr. 40: 148-158 DOI ScienceOn |
10 | Page, A. L., R. H. Miller, and D. R. Keeney. 1982. Methods of Soil Analysis. Part 2: Chemical and Microbiological Properties, 2nd ed. American Society of Agronomy, Madison, WI, U.S.A |
11 | Phelps, C. D., L. J. Kerkhof, and L. Y. Young. 1998. Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol. Ecol. 27: 269-279 |
12 | Tanner, M. A., C. L. Everett, W. J. Coleman, M. M. Yang, and D. C. Youvan. 2000. Complex microbial consortia inhabiting hydrogen sulfide-rich black mud from marine coastal environments. Biotechnol. et alia 8: 1-16 |
13 | Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65: 3982-3989 |
14 | Li, L., C. Kato, and K. Horikoshi. 1999. Bacterial diversity in deep-sea sediments from different depths. Biodivers. Conserv. 8: 659-677 |
15 | Liu, W. T., T. L. Marsh, H. Cheng, and L. J. Forney. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 63: 4516- 4522 |
16 | Huber, J. A., D. A. Butterfield, and J. A. Baross. 2003. Bacterial diversity in a subseafloor habitat following a deepsea volcanic eruption. FEMS Microbiol. Ecol. 43: 393-409 |
17 | Llobet-Brossa, E., R. Rossello-Mora, and R. Amann. 1998. Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 64: 2691-2696 |
18 | MacNaughton, S. J., J. R. Stephen, A. D. Venosa, G. A. Davis, Y. J. Chang, and D. C. White. 1999. Microbial population changes during bioremediation of an experimental oil spill. Appl. Environ. Microbiol. 65: 3566-3574 |
19 | Carling, P. A. 1982. Temporal and spatial variation in intertidal sedimentation rates. Sedimentol. 29: 17-23 DOI |
20 | Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791 |
21 | Hedlund, B. P., A. D. Geiselbrecht, T. J. Bair, and J. T. Staley. 1999. Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Appl. Environ. Microbiol. 65: 251-259 |
22 | Lee, W. J. and K. S. Bae. 2001. The phylogenetic relationship of several oscillatorian cyanobacteria, forming blooms at Daecheong reservoirs, based on partial 16S rRNA gene sequences. J. Microbiol. Biotechnol. 11: 504-507 |
23 | Derakshani, M., T. Lukow, and W. Liesack. 2001. Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms. Appl. Environ. Microbiol. 67: 623-631 |
24 | Holben, W. E., J. K. Jansso, B. K. Chelm, and J. M. Tiedje. 1988. DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Environ. Microbiol. 54: 703-711 |
25 | Urakawa, H., K. Kita-Tsukamoto, and K. Ohwada. 1999. Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis. Microbiology 145: 3305-3315 |
26 | Park, J., B., H. Lee, W., S.-Y. Lee, J. O. Lee, I. S. Bang, E. S. Choi, D. H. Park, and Y. K. Park. 2002. Microbial community analysis of 5-stage biological nutrient removal process with step feed system. J. Microbiol. Biotechnol. 12: 929-935 |
27 | Sahm, K., C. Knoblauch, and R. Amann. 1999. Phylogenetic affiliation and quantification of psychrophilic sulfatereducing isolates in marine arctic sediments. Appl. Environ. Microbiol. 65: 3976-3981 |
28 | Yi, H. and J. Chun. 2002. Remarkable cultured bacterial biodiversity in getbol, the tidal flat of Korea. IUMS World Congress, Paris, France |
29 | Choi, H.-P., H.-J. Kang, H.-C. Seo, and H.-C. Sung. 2002. Isolation and identification of photosynthetic bacterium useful for waste water treatment. J. Microbiol. Biotechnol. 12: 643-648 |
30 | Devereux, R., M. Delaney, F. Widdel, and D. A. Stahl. 1989. Natural relationships among sulfate-reducing eubacteria. J. Bacteriol. 171: 6689-6695 |
31 | Jorgensen, B. B. 1982. Ecology of the bacteria of the sulphur cycle with special reference to anoxic-oxic interface environments. Philos. Trans. R Soc. Lond. B Biol. Sci. 298: 543-561 DOI PUBMED ScienceOn |
32 | Chun, J. and M. Goodfellow. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 45: 240-245 |
33 | Ravenschlag, K., K. Sahm, C. Knoblauch, B. B. Jorgensen, and R. Amann. 2000. Community structure, cellular rRNA content, and activity of sulfate- reducing bacteria in marine arctic sediments. Appl. Environ. Microbiol. 66: 3592-3602 |
34 | Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25: 109-111 |
35 | Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425 |
36 | Jukes, T. H. and C. R. Cantor. 1969. Evolution of protein molecules, pp. 21-132. In Munro, H. N. (ed.), Mammalian Protein Metabolism. Academic Press, New York, U.S.A |
37 | LaPara, T. M., C. H. Nakatsu, L. Pantea, and J. E. Alleman. 2000. Phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. Appl. Environ. Microbiol. 66: 3951-3959 |
38 | Torsvik, V., J. Goksoyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56: 782- 787 |
39 | Crump, B. C., E. V. Armbrust, and J. A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 65: 3192-3204 |
40 | Yanagibayashi, M., Y. Nogi, L. Li, and C. Kato. 1999. Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiol. Lett. 170: 271-279 |
41 | Smith, W. 1993. Ecological actions of sulfate-reducing bacteria, pp. 161-188. In Odom, J. M. and R. Singleton (eds.), The Sulfate-Reducing Bacteria: Contemporary Perspectives. Springer-Verlag, New York, U.S.A |
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